In this paper, we develop fast procedures for solving linear systems arising from discretization of ordinary and partial differential equations with Caputo fractional derivative w.r.t time variable. First, we consider a finite difference scheme to solve a two-sided fractional ordinary equation. Furthermore, we present a fast solution technique to accelerate Toeplitz matrix-vector multiplications arising from finite difference discretization. This fast solution technique is based on a fast Fourier transform and depends on the special structure of coefficient matrices, and it helps to reduce the computational work from $O(N^{3})$ required by traditional methods to $O(Nlog^{2}N)$ and the memory requirement from $O(N^{2})$ to $O(N)$ without using any lossy compression, where $N$ is the number of unknowns. Two finite difference schemes to solve time fractional hyperbolic equations with different fractional order $gamma$ are considered. We present a fast solution technique depending on the special structure of coefficient matrices by rearranging the order of unknowns. It helps to reduce the computational work from $O(N^2M)$ required by traditional methods to $O(N$log$^{2}N)$ and the memory requirement from $O(NM)$ to $O(N)$ without using any lossy compression, where $N=tau^{-1}$ and $tau$ is the size of time step, $M=h^{-1}$ and $h$ is the size of space step. Importantly, a fast method is employed to solve the classical time fractional diffusion equation with a lower coast at $O(MN$log$^2N)$, where the direct method requires an overall computational complexity of $O(N^2M)$. Moreover, the applicability and accuracy of the scheme are demonstrated by numerical experiments to support our theoretical analysis.
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